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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/overlaps_8cpp_source.html below:

NCBI C++ ToolKit: src/app/read_blast_result/overlaps.cpp Source File

from = ext_rna->exons[0].from;

to = ext_rna->exons[ext_rna->exons.size()-1].to;

(;seq!=seqs.end(); seq++, nseq++)

from2 = seq->exons[0].from;

to2 = seq->exons[seq->exons.size()-1].to;

over_origin = seq->exons.size()>1 && to2-from2 >

/2;

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<<

;

(to2>=from || over_origin)

(from2<=to || over_origin)

TSimpleSeqs::iterator seq2 = seq;

(;seq2!=seqs.end(); seq2++)

from2 = seq2->exons[0].from;

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<<

;

(ext_rna, seq2, this_overlap);

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<< this_overlap <<

;

best_seq.push_back(*seq2);

from = ext_rna->exons[0].from;

to = ext_rna->exons[ext_rna->exons.size()-1].to;

ext_rna_range_stream; ext_rna_range_stream << from <<

<< to <<

;

ext_rna_range = ext_rna_range_stream.str();

TSimpleSeqs::iterator& best_seq = seq;

(;seq!=seqs.end(); seq++, nseq++)

from2 = seq->exons[0].from;

to2 = seq->exons[seq->exons.size()-1].to;

ext_rna_range_stream2; ext_rna_range_stream2 << from2 <<

<< to2 <<

;

ext_rna_range2 = ext_rna_range_stream2.str();

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<<

;

TSimpleSeqs::iterator seq2 = seq;

(;seq2!=seqs.end(); seq2++)

from2 = seq2->exons[0].from;

to2 = seq2->exons[seq->exons.size()-1].to;

ext_rna_range_stream2; ext_rna_range_stream2 << from2 <<

<< to2 <<

;

ext_rna_range2 = ext_rna_range_stream2.str();

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<<

;

(from2>to)

;

(ext_rna, seq2, this_overlap);

<<

<< ext_rna_range <<

<<

<< ext_rna_range2 <<

<<

<< this_overlap <<

;

(this_overlap>overlap)

overlap=this_overlap;

(TSimplePairs::const_iterator e1=seq1->exons.begin(); e1!=seq1->exons.end(); e1++)

(TSimplePairs::const_iterator e2=seq2->exons.begin(); e2!=seq2->exons.end(); e2++)

o =

(e2->to, e1->to)-

(e1->from, e2->from)+1;

( !(*gen_feature)->GetData().IsFtable() )

;

( !(*gen_feature)->GetData().IsFtable() )

;

lres =

((*gen_feature)->GetData().GetFtable());

(seq_interval, from2, to2, strand2);

( !(*f1)->GetData().IsRna() )

;

lres=

(seq_interval, (*f1)->GetLocation(), overlap);

(trna_type.size()>0) name1 = trna_type;

((*f1)->GetLocation(), from1, to1, strand1);

min1, min2, max1, max2;

min1 =

(from1, to1);

min2 =

(from2, to2);

max1 =

(from1, to1);

max2 =

(from2, to2);

left_frame = (from1-1)%3+1;

right_frame = (from2-1)%3+1;

report->

= overlap;

report->

= &((*f1)->GetLocation());

report->

= &seq_interval;

bufferchar[20480]; memset(bufferchar, 0, 20480);

strstream

(bufferchar, 20480);

<<

<< name1 <<

<<

(seq) <<

<<

;

buff_misc_feat_protein

<<

<<

(seq) <<

<< name1 <<

<<

;

misc_feat_rna << buff_misc_feat_rna.str() <<

;

misc_feat_protein << buff_misc_feat_protein.str() <<

;

(

())

<<

<< buff_misc_feat_rna.str() <<

;

(

())

<<

<< buff_misc_feat_protein.str() <<

;

[n1].problems.push_back(problem);

removeit=

;

removen =

;

<<

<< n1 <<

<<

;

<<

<< n1 <<

<<

;

<<

<< n2 <<

<<

;

[removen].problems.push_back(problemCOH);

[removen].problems.push_back(problemCOH);

<<

<< removen <<

<<

<<

<< removen <<

;

( !(*f1)->GetData().IsRna() )

;

( !(*f1)->GetData().GetRna().CanGetExt() )

;

{ type1 =

((*f1)->GetData().GetRna());}

<<

<<

;

(type1.size()==0)

;

n2=

;

(n1==n2)

;

<

t1,

t2>

from1, to1, from2, to2;

min1, min2, max1, max2;

min1 =

(from1, to1);

max1 =

(from1, to1);

min2 =

(from2, to2);

max2 =

(from2, to2);

overlap_start, overlap_end;

overlap_end =

(max1, max2);

overlap_start =

(min1, min2);

result2 = overlap_end >= overlap_start;

(!result2)

;

overlap+=overlap_end - overlap_start + 1;

min1, min2, max1, max2;

min2 =

(from2, to2);

max2 =

(from2, to2);

min1 =

(from1, to1);

max1 =

(from1, to1);

overlap_start, overlap_end;

overlap_end =

(max1, max2);

overlap_start =

(min1, min2);

result2 = overlap_end >= overlap_start;

(result2)

=

;

overlap+=overlap_end - overlap_start + 1;

from1, to1, from2, to2;

min1, min2, max1, max2;

getFromTo( *i1, from1, to1, strand1);

min1 =

(from1, to1);

max1 =

(from1, to1);

getFromTo( *i2, from2, to2, strand2);

min2 =

(from2, to2);

max2 =

(from2, to2);

(min2<=min1 && max2>=max1)

(PrintDetails())

<<

<< from1 <<

<< to1 <<

<< from2 <<

<< to2 <<

(!hasGenomicLocation(left))

;

(!hasGenomicLocation(right))

;

& left_genomic_int = getGenomicLocation(left);

& right_genomic_int = getGenomicLocation(right);

from1, to1, from2, to2;

getFromTo(left_genomic_int, from1, to1, left_strand);

getFromTo(right_genomic_int, from2, to2, right_strand);

left_frame=-0xFF, right_frame=-0xFF;

(left_genomic_int.

())

left_frame = (from1-1)%3+1;

(right_genomic_int.

())

right_frame = (from2-1)%3+1;

(

((

)to1, (

)to2)-

((

)from2, (

)from1)

complete_overlaps =

;

= overlaps(left_genomic_int, right_genomic_int, scratch_overlap);

left_covered_by_right=

;

right_covered_by_left=

;

(

) complete_overlaps = (left_covered_by_right=complete_overlap(left_genomic_int, right_genomic_int))

|| (right_covered_by_left=complete_overlap(right_genomic_int, left_genomic_int));

(PrintDetails())

<<

<< space

<<

<< complete_overlaps

<<

<<

(

&& scratch_overlap >= m_cds_overlapThreshold)

report->

= space;

bufferchar[20480]; memset(bufferchar, 0, 20480);

strstream

(bufferchar, 20480);

printOverlapReport(report,

);

<<

<< GetProtName(left)

<<

<< GetProtName(right) <<

<<

<<

;

<<

<< GetProtName(right)

<<

<< GetProtName(left) <<

<<

<<

;

(complete_overlaps)

(report->

.find(

)!=string::npos && left_covered_by_right && !right_covered_by_left)

<<

<<

<< qname <<

<<

m_diag[qname].problems.push_back(problemCOH);

m_diag[qname].problems.push_back(problemCO);

<<

(report->

.find(

)!=string::npos && right_covered_by_left)

<<

<<

<< qrname <<

<<

m_diag[qrname].problems.push_back(problemCOH);

m_diag[qrname].problems.push_back(problemCO);

<<

m_diag[qname].problems.push_back(problemO_l);

m_diag[qrname].problems.push_back(problemO_r);

m_diag[qname].problems.push_back(problemO_l);

m_diag[qrname].problems.push_back(problemO_r);

void GetLabel(string *label) const

static bool PrintDetails(int current_verbosity=m_current_verbosity)

static string GetProtName(const CBioseq &seq)

CConstBeginInfo ConstBegin(void)

void GetLocMap(LocMap &loc_map, const CSeq_annot::C_Data::TFtable &feats)

static void IncreaseVerbosity(void)

bool overlaps_na(const CBioseq::TAnnot &annots)

static void printOverlapReport(distanceReportStr *report, ostream &out=NcbiCout)

int find_overlap(TSimpleSeqs::iterator &seq, const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs &seqs, int &overlap)

bool complete_overlap(const CSeq_loc &l1, const CSeq_loc &l2)

static int m_rna_overlapThreshold

static void DecreaseVerbosity(void)

int overlaps(const TSimpleSeqs::iterator &seq1, const TSimpleSeqs::iterator &seq2, int &overlap)

static const CSeq_loc & getGenomicLocation(const CBioseq &seq)

bool overlaps_prot_na(CBioseq &seq, const CBioseq::TAnnot &annots)

static void getFromTo(const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)

bool match_na(const CSeq_feat &f1, const string &type1)

void append_misc_feature(CBioseq_set::TSeq_set &seqs, const string &name, EProblem problem_type)

namespace ncbi::objects::

Template class for iteration on objects of class C (non-medifiable version)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

@ eOverlap

CSeq_locs overlap.

EType

type of RNA feature

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

const TGene & GetGene(void) const

Get the variant data.

ENa_strand

strand of nucleic acid

bool IsInt(void) const

Check if variant Int is selected.

list< CRef< CSeq_entry > > TSeq_set

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

unsigned int

A callback function used to compare two keys in a database.

@ eMyFeatureType_normal_tRNA

@ eMyFeatureType_atypical_tRNA

@ eMyFeatureType_pseudo_tRNA

@ eMyFeatureType_hypo_CDS

string get_trna_string(const CSeq_feat &feat)

string GetStringDescr(const CBioseq &bioseq)

string Get3type(const CRNA_ref &rna)

EMyFeatureType get_my_feat_type(const CSeq_feat &feat, const LocMap &loc_map)

string get_title(const CBioseq &seq)

EMyFeatureType get_my_seq_type(const CBioseq &seq)

string GetLocusTag(const CSeq_feat &f, const LocMap &loc_map)

CBioseq_set::TSeq_set * get_parent_seqset(const CBioseq &seq)

string GetRNAname(const CSeq_feat &feat)

list< TSimpleSeq > TSimpleSeqs

string GetRRNAtype(const CRNA_ref &rna)

string printed_range(const TSeqPos from2, const TSeqPos to2)

CRef< const CSeq_loc > loc1

CRef< const CSeq_loc > loc2

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